Add new MP input sets / concurrently update MatPES POTCARs (#3916)

* add new MP24 input sets

* pre-commit auto-fixes

* typing for config updates

* pre-commit auto-fixes

* skip json in codespell check

* still trying to skip codespell json checks

* update base PBE 64 pseudopotentials, add hash for MP24 sets to sets

* fix matpes set to remove the GGA tag for r2SCAN runs

* slight tweak

* pre-commit auto-fixes

* fixes

* pre-commit auto-fixes

* disable auto_ismear

* fix bandap --> kspacing

* pre-commit auto-fixes

* Add GGA_COMPAT False tag

* Add full test, clean up vdw stuff (prev unused)

* Add citation info

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Shyue Ping Ong <[email protected]>

Author: 3 people

src/pymatgen/io/vasp/MP24RelaxSet.yaml

@@ -0,0 +1,31 @@
+# Default VASP settings for calculations in the Materials Project
+# using the Regularized-Restored Strongly Constrained and Appropriately
+# Normed functional (r2SCAN).
+PARENT: PBE64Base
+INCAR:
+  ALGO: Normal
+  EDIFF: 1.e-05
+  EDIFFG: -0.02
+  ENAUG: 1360
+  ENCUT: 680
+  GGA_COMPAT: False
+  IBRION: 2
+  ISIF: 3
+  ISMEAR: 0 # included to have some reasonable default
+  ISPIN: 2
+  KSPACING: 0.22 # included to have some reasonable default
+  LAECHG: True
+  LASPH: True
+  LCHARG: True
+  LELF: False # LELF = True restricts calculation to KPAR = 1
+  LMAXMIX: 6 # per benchmark
+  LMIXTAU: True
+  LORBIT: 11
+  LREAL: False # per benchmark
+  LVTOT: True
+  LWAVE: False
+  METAGGA: R2SCAN
+  NELM: 200
+  NSW: 99
+  PREC: Accurate
+  SIGMA: 0.05 # included to have some reasonable default

src/pymatgen/io/vasp/PBE64Base.yaml

@@ -11,7 +11,7 @@ POTCAR:
   At: At
   Au: Au
   B: B
-  Ba: Ba_sv
+  Ba: Ba_sv_GW
   Be: Be_sv
   Bi: Bi
   Br: Br
@@ -26,8 +26,8 @@ POTCAR:
   Cr: Cr_pv
   Cs: Cs_sv
   Cu: Cu_pv
-  Dy: Dy_3
-  Er: Er_3
+  Dy: Dy_h
+  Er: Er_h
   Eu: Eu
   F: F
   Fe: Fe_pv
@@ -39,7 +39,7 @@ POTCAR:
   He: He
   Hf: Hf_pv
   Hg: Hg
-  Ho: Ho_3
+  Ho: Ho_h
   I: I
   In: In_d
   Ir: Ir
@@ -54,7 +54,7 @@ POTCAR:
   N: N
   Na: Na_pv
   Nb: Nb_pv
-  Nd: Nd_3
+  Nd: Nd_h
   Ne: Ne
   Ni: Ni_pv
   Np: Np
@@ -64,9 +64,9 @@ POTCAR:
   Pa: Pa
   Pb: Pb_d
   Pd: Pd
-  Pm: Pm_3
+  Pm: Pm_h
   Po: Po_d
-  Pr: Pr_3
+  Pr: Pr_h
   Pt: Pt
   Pu: Pu
   Ra: Ra_sv
@@ -80,22 +80,22 @@ POTCAR:
   Sc: Sc_sv
   Se: Se
   Si: Si
-  Sm: Sm_3
+  Sm: Sm_h
   Sn: Sn_d
   Sr: Sr_sv
   Ta: Ta_pv
-  Tb: Tb_3
+  Tb: Tb_h
   Tc: Tc_pv
   Te: Te
   Th: Th
   Ti: Ti_pv
   Tl: Tl_d
-  Tm: Tm_3
+  Tm: Tm_h
   U: U
   V: V_pv
   W: W_sv
-  Xe: Xe
+  Xe: Xe_GW
   Y: Y_sv
-  Yb: Yb_3
+  Yb: Yb_h
   Zn: Zn
   Zr: Zr_sv

src/pymatgen/io/vasp/sets.py

@@ -84,7 +84,10 @@
 
 
 def _load_yaml_config(fname):
-    config = loadfn(f"{MODULE_DIR}/{fname}.yaml")
+    fname = f"{MODULE_DIR}/{fname}"
+    if not fname.endswith(".yaml"):
+        fname += ".yaml"
+    config = loadfn(fname)
     if "PARENT" in config:
         parent_config = _load_yaml_config(config["PARENT"])
         for k, v in parent_config.items():
@@ -623,7 +626,11 @@ def incar(self) -> Incar:
             elif key == "KSPACING" and self.auto_kspacing:
                 # Default to metal if no prev calc available
                 bandgap = 0 if self.bandgap is None else self.bandgap
-                incar[key] = auto_kspacing(bandgap, self.bandgap_tol)
+                if new_kspacing := getattr(self, "kspacing_update", None):
+                    # allow custom KSPACING update
+                    incar[key] = new_kspacing
+                else:
+                    incar[key] = auto_kspacing(bandgap, self.bandgap_tol)
 
             else:
                 incar[key] = setting
@@ -1294,7 +1301,7 @@ class MPRelaxSet(VaspInputSet):
 
 @due.dcite(
     Doi("10.1021/acs.jpclett.0c02405"),
-    description="AccurAccurate and Numerically Efficient r2SCAN Meta-Generalized Gradient Approximation",
+    description="Accurate and Numerically Efficient r2SCAN Meta-Generalized Gradient Approximation",
 )
 @due.dcite(
     Doi("10.1103/PhysRevLett.115.036402"),
@@ -1352,7 +1359,7 @@ class MPScanRelaxSet(VaspInputSet):
 
         James W. Furness, Aaron D. Kaplan, Jinliang Ning, John P. Perdew, and Jianwei Sun.
         Accurate and Numerically Efficient r2SCAN Meta-Generalized Gradient Approximation.
-        The Journal of Physical Chemistry Letters 0, 11 DOI: 10.1021/acs.jpclett.0c02405
+        The Journal of Physical Chemistry Letters 11, 8208-8215 (2022) DOI: 10.1021/acs.jpclett.0c02405
     """
 
     bandgap: float | None = None
@@ -1375,6 +1382,149 @@ def __post_init__(self) -> None:
                 self._config_dict["INCAR"].pop(k, None)
 
 
+@dataclass
+class MP24RelaxSet(VaspInputSet):
+    """
+    Materials Project relax set after a 2023-2024 benchmarking effort.
+
+    By default, this uses r2SCAN as the xc functional.
+    For discussion around this benchmarking effort, see:
+    https://github.com/materialsproject/foundation/pull/26
+
+    Citation info:
+    - r2SCAN:
+        James W. Furness, Aaron D. Kaplan, Jinliang Ning, John P. Perdew, and Jianwei Sun.
+        Accurate and Numerically Efficient r2SCAN Meta-Generalized Gradient Approximation.
+        J. Phys. Chem. Lett. 11, 8208-8215 (2022) DOI: 10.1021/acs.jpclett.0c02405
+    - r2SCAN-rVV10:
+        Jinliang Ning, Manish Kothakonda, James W. Furness, Aaron D. Kaplan, Sebastian Ehlert,
+            Jan Gerit Brandenburg, John P. Perdew, and Jianwei Sun.
+        Workhorse minimally empirical dispersion-corrected density functional with tests for
+            weakly bound systems: r2SCAN+rVV10.
+        Phys. Rev. B 106, 075422 (2022) DOI: 10.1103/PhysRevB.106.075422
+    - r2SCAN-D4:
+        Sebastian Ehlert, Uwe Huniar, Jinliang Ning, James W. Furness, Jianwei Sun,
+            Aaron D. Kaplan, John P. Perdew, and Jan Gerit Brandenburg.
+        r2SCAN-D4: Dispersion corrected meta-generalized gradient approximation for general chemical applications.
+        J. Chem. Phys. 154, 061101 (2021) DOI: 10.1063/5.0041008
+    - PBE:
+        John P. Perdew, Kieron Burke, and Matthias Ernzerhof,
+        Generalized Gradient Approximation Made Simple,
+        Phys. Rev. Lett. 77, 3865 (1996) DOI: 10.1103/PhysRevLett.77.3865
+    - PBEsol:
+        John P. Perdew, Adrienn Ruzsinszky, Gábor I. Csonka, Oleg A. Vydrov,
+            Gustavo E. Scuseria, Lucian A. Constantin, Xiaolan Zhou, and Kieron Burke.
+        Restoring the Density-Gradient Expansion for Exchange in Solids and Surfaces.
+        Phys. Rev. Lett. 100, 136406 (2009) DOI: 10.1103/PhysRevLett.100.136406
+    - PBE-D4 and PBEsol-D4:
+        Eike Caldeweyher,Jan-Michael Mewes, Sebastian Ehlert, and Stefan Grimme.
+        Extension and evaluation of the D4 London-dispersion model for periodic systems.
+        Phys. Chem. Chem. Phys. 22, 8499-8512 (2020) DOI: 10.1039/D0CP00502A
+    """
+
+    xc_functional: Literal["r2SCAN", "PBE", "PBEsol"] = "r2SCAN"
+    dispersion: Literal["rVV10", "D4"] | None = None
+    CONFIG = _load_yaml_config("MP24RelaxSet")
+    auto_ismear: bool = False
+    auto_kspacing: bool = True
+    inherit_incar: bool = False
+
+    def __post_init__(self) -> None:
+        super().__post_init__()
+
+        to_func = {
+            "r2SCAN": "R2SCAN",
+            "PBE": "PE",
+            "PBEsol": "PS",
+        }
+
+        config_updates: dict[str, Any] = {}
+        if self.xc_functional == "r2SCAN":
+            config_updates |= {"METAGGA": to_func[self.xc_functional]}
+            self._config_dict["INCAR"].pop("GGA", None)
+        elif self.xc_functional in ["PBE", "PBEsol"]:
+            config_updates |= {"GGA": to_func[self.xc_functional]}
+            self._config_dict["INCAR"].pop("METAGGA", None)
+        else:
+            raise ValueError(f"Unknown XC functional {self.xc_functional}!")
+
+        if self.dispersion == "rVV10":
+            if self.xc_functional == "r2SCAN":
+                config_updates |= {"BPARAM": 11.95, "CPARAM": 0.0093, "LUSE_VDW": True}
+            else:
+                raise ValueError(
+                    "Use of rVV10 with functionals other than r2 / SCAN is not currently supported in VASP."
+                )
+
+        elif self.dispersion == "D4":
+            d4_pars = {
+                "r2SCAN": {
+                    "S6": 1.0,
+                    "S8": 0.60187490,
+                    "A1": 0.51559235,
+                    "A2": 5.77342911,
+                },
+                "PBE": {
+                    "S6": 1.0,
+                    "S8": 0.95948085,
+                    "A1": 0.38574991,
+                    "A2": 4.80688534,
+                },
+                "PBEsol": {
+                    "S6": 1.0,
+                    "S8": 1.71885698,
+                    "A1": 0.47901421,
+                    "A2": 5.96771589,
+                },
+            }
+            config_updates |= {"IVDW": 13, **{f"VDW_{k}": v for k, v in d4_pars[self.xc_functional].items()}}
+
+        if len(config_updates) > 0:
+            self._config_dict["INCAR"].update(config_updates)
+
+    @staticmethod
+    def _sigmoid_interp(
+        bg, min_dk: float = 0.22, max_dk: float = 0.5, shape: float = 0.43, center: float = 4.15, fac: float = 12.0
+    ):
+        delta = shape * (bg - center)
+        sigmoid = delta / (1.0 + delta**fac) ** (1.0 / fac)
+        return 0.5 * (min_dk + max_dk + (max_dk - min_dk) * sigmoid)
+
+    def _multi_sigmoid_interp(
+        self,
+        bandgap: float,
+        dks: tuple[float, ...] = (0.22, 0.44, 0.5),
+        shape: tuple[float, ...] = (1.1, 2.5),
+        center: tuple[float, ...] = (2.35, 6.1),
+        fac: tuple[float, ...] = (8, 8),
+        bg_cut: tuple[float, ...] = (4.5,),
+    ):
+        if bandgap < self.bandgap_tol:
+            return dks[0]
+
+        min_bds = [self.bandgap_tol, *bg_cut]
+        max_bds = [*bg_cut, np.inf]
+
+        for icut, min_bd in enumerate(min_bds):
+            if min_bd <= bandgap < max_bds[icut]:
+                return self._sigmoid_interp(
+                    bandgap,
+                    min_dk=dks[icut],
+                    max_dk=dks[icut + 1],
+                    shape=shape[icut],
+                    center=center[icut],
+                    fac=fac[icut],
+                )
+
+        return None
+
+    @property
+    def kspacing_update(self):
+        if self.bandgap is None:
+            return 0.22
+        return self._multi_sigmoid_interp(self.bandgap)
+
+
 @dataclass
 class MPMetalRelaxSet(VaspInputSet):
     """
@@ -1571,7 +1721,8 @@ def __post_init__(self) -> None:
             )
 
         if self.xc_functional.upper() == "R2SCAN":
-            self._config_dict["INCAR"].update({"METAGGA": "R2SCAN", "ALGO": "ALL", "GGA": None})
+            self._config_dict["INCAR"].update({"METAGGA": "R2SCAN", "ALGO": "ALL"})
+            self._config_dict["INCAR"].pop("GGA", None)
         if self.xc_functional.upper().endswith("+U"):
             self._config_dict["INCAR"]["LDAU"] = True
 
@@ -1601,6 +1752,7 @@ class MPScanStaticSet(MPScanRelaxSet):
     def incar_updates(self) -> dict[str, Any]:
         """Updates to the INCAR config for this calculation type."""
         updates: dict[str, Any] = {
+            "ALGO": "Fast",
             "LREAL": False,
             "NSW": 0,
             "LORBIT": 11,
@@ -1626,6 +1778,49 @@ def incar_updates(self) -> dict[str, Any]:
         return updates
 
 
+@dataclass
+class MP24StaticSet(MP24RelaxSet):
+    """Create input files for a static calculation using MP24 parameters.
+
+    For class information, refer to `MP24RelaxSet`.
+    If you use this set, please consider citing the appropriate papers in `MP24RelaxSet`.
+
+    Args:
+        structure (Structure): Structure from previous run.
+        bandgap (float): Bandgap of the structure in eV. The bandgap is used to
+            compute the appropriate k-point density and determine the smearing settings.
+        lepsilon (bool): Whether to add static dielectric calculation
+        lcalcpol (bool): Whether to turn on evaluation of the Berry phase approximations
+            for electronic polarization.
+        **kwargs: Keywords supported by MP24RelaxSet.
+    """
+
+    lepsilon: bool = False
+    lcalcpol: bool = False
+    inherit_incar: bool = False
+    auto_kspacing: bool = True
+
+    @property
+    def incar_updates(self) -> dict[str, Any]:
+        """Updates to the INCAR config for this calculation type."""
+        updates: dict[str, Any] = {
+            "NSW": 0,
+            "LORBIT": 11,
+            "ISMEAR": -5,
+        }
+
+        if self.lepsilon:
+            # LPEAD=T: numerical evaluation of overlap integral prevents
+            # LRF_COMMUTATOR errors and can lead to better expt. agreement
+            # but produces slightly different results
+            updates |= {"IBRION": 8, "LEPSILON": True, "LPEAD": True, "NSW": 1, "NPAR": None}
+
+        if self.lcalcpol:
+            updates["LCALCPOL"] = True
+
+        return updates
+
+
 @dataclass
 class MPHSEBSSet(VaspInputSet):
     """Implementation of a VaspInputSet for HSE band structure computations.